Abstract
Alpha solenoid proteins play a key role in regulating the classical nuclear import pathway, recognizing a target protein and transporting it into the nucleus. Importin-α (Impα) is the solenoid responsible for cargo protein recognition, and it has been extensively studied by X-ray crystallography to understand the binding specificity. To comprehend the main motions of Impα and to extend the information about the critical interactions during carrier-cargo recognition, we surveyed different conformational states based on molecular dynamics (MD) and normal mode (NM) analyses. Our model of study was a crystallographic structure of Impα complexed with the classical nuclear localization sequence (cNLS) from nucleoplasmin (Npl), which was submitted to multiple 100 ns of MD simulations. Representative conformations were selected for calculating the 87 lowest frequencies NMs of vibration, and a displacement approach was applied along each NM. Based on geometric criteria, using the radius of curvature and inter-repeat angles as the reference metrics, the main motions of Impα were described. Moreover, we determined the salt bridges, hydrogen bonds and hydrophobic interactions in the Impα-NplNLS interface. Our results show the bending and twisting motions participating in the recognition of nuclear proteins, allowing the accommodation and adjustment of a classical bipartite NLS sequence. The essential contacts for the nuclear import were also described and were mostly in agreement with previous studies, suggesting that the residues in the cNLS linker region establish important contacts with Impα adjusting the cNLS backbone. The MD simulations combined with NM analysis can be applied to the Impα-NLS system to help understand interactions between Impα and cNLSs and the analysis of non-classic NLSs.
Highlights
Solenoid proteins are molecules composed of structural motifs that are arranged in tandem, creating a superhelical architecture
The trajectories obtained from the three Impα-nucleoplasmin NLS (NplNLS) molecular dynamics (MD) simulations were clustered into three reference structures (67,730 ps, 207,080 ps and 274,970 ps), each one exhibiting a similar frame-frequency among simulations, indicating a likely convergence of the MDs (S2 Fig)
Reference structure 207,080ps was the most representative in the simulations and was more similar to the X-ray-solved NplNLS structure based on the backbone root-mean square deviation (RMSD) values (S1 Table) obtained from the structural alignment of the nuclear localization sequence (NLS) (S3 Fig)
Summary
Solenoid proteins are molecules composed of structural motifs that are arranged in tandem, creating a superhelical architecture. One of the most studied pathways is the classical nuclear import pathway, which requires the interaction between the solenoid Importin-α (Impα) and Importin-β (Impβ) proteins, followed by the assembly of the cargo protein to Impα [6,7,8,9,10]. This trimeric complex is translocated through the nuclear pore complex (NPC), and the cargo protein is delivered into the cell nucleus mediated by Ran-GTP-dependent steps of protein-protein interactions [11, 12]. A final step is the recycling of both Impα and Impβ back to the cytoplasm
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